The role of homeobox gene, Prox 1 in vertebrate eye development and regeneration was studied. The zebrafish Prox 1 gene was isolated and characterized and its expression pattern was studied by whole-mount immunohistochemistry and in situ hybridization. Expression of Prox 1 was first detected in the ten-somite stage embryos in the ectoderm overlaying the eye buds. As embryogenesis proceeds, Prox 1 expression was also detected in muscle pioneer cells, forebrain-midbrain boundary, ventral hindbrain, and selected cells of the ventral spinal cord. A partial Prox 1 cDNA was isolated from the newt. In the process of lens regeneration in the newt, Prox 1 protein was found to be selectively expressed in the regenerating competent cells of the dorsal iris but not in the cells of ventral iris.